Antonino Ingargiola edited Introduction.tex  about 8 years ago

Commit id: b70470fc5f14572d9bbed4a7c68bafd586d9e402

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(section~\ref{sec:concepts}).  In section~\ref{sec:analysis}, we illustrate the steps involved  in smFRET burst analysis: (i) data loading (section~\ref{sec:dataload}), )ii) (ii)  definition of the excitation alternation periods (section~\ref{sec:alternation}), (iii) background  correction (section~\ref{sec:bg_calc}), (iv) burst search (section~\ref{sec:burstsearch}),  (v) burst selection (section~\ref{sec:burstsel}) and (vi) FRET histogram fitting (section~\ref{sec:fretfit}).  The aim of this section is to illustrate the specificities and trade-off involved in various approaches  with sufficient details to enable readers new to the field (or Jupyter Notebooks) to customize the analysis for their own needs. Section~\ref{sec:bva} walks the reader thorough implementing  Burst Variance Analysis (BVA)~\cite{Torella_2011}, as an example of implementation of an advanced data processing technique. Finally, section~\ref{sec:conclusions} summarizes what we believe to be  the strengths of FRETBursts software. 

links to relevant sections of documentation and other web resources  are displayed as ``(link)''.  In order to make the text more legible,  we have concentrated python-specific Python-specific  details in subsections entitled \textit{Python details}. These subsections provide deeper insights for readers  already familiar with python Python  and can be initially skipped by readers who are not. Finally, note that all commands here reported can be found in the  accompanying notebooks  (\href{https://github.com/tritemio/fretbursts_paper}{link}).